8-9329732-A-G

Position:

• chr8-9329732-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520390.1(PPP1R3B-DT):​n.766-2672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,210 control chromosomes in the GnomAD database, including 59,468 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (59468 hom., cov: 32)
• Consequence: PPP1R3B-DT ENST00000520390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

PPP1R3B-DT (HGNC:56150): (PPP1R3B divergent transcript)

LOC157273 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC157273	NR_040039.1	n.766-2672A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3B-DT	ENST00000518619.1	n.196+3429A>G		intron_variant		3
PPP1R3B-DT	ENST00000520255.6	n.739+3429A>G		intron_variant		3
PPP1R3B-DT	ENST00000520390.1	n.766-2672A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134196 AN: 152092 Hom.: 59441 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.884

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.882 AC: 134276 AN: 152210 Hom.: 59468 Cov.: 32 AF XY: 0.878 AC XY: 65310 AN XY: 74400

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.879

Alfa AF: 0.881 Hom.: 25191

Bravo AF: 0.877

Asia WGS AF: 0.924 AC: 3214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.071
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1461729; hg19: chr8-9187242;